Try to find the problem that causes coredump

Author: Andreas Tille <tille@debian.org>

Last-Update: Fri, 28 Sep 2018 14:24:07 +0200

Bug-Debian: https://bugs.debian.org/909530

Description: Try to find the problem that causes coredump

--- a/t_coffee_source/util_lib/util_constraints_list.c

+++ b/t_coffee_source/util_lib/util_constraints_list.c

@@ -1335,6 +1335,7 @@ Constraint_list *  undump_constraint_lis

 	int *entry, b, c, e, tot;

 	FILE *fp;

+fprintf (stderr, "\nDEBUG %s(%i):  file = %s", __FILE__, __LINE__, file);

 	if (!CL || !CL->residue_index)return CL;

 	entry=(int*)vcalloc ( CL->entry_len+1, sizeof (int));

 	fp=vfopen (file, "r");

@@ -2147,25 +2148,29 @@ Constraint_list* fork_read_n_constraint_

 		int pid;

 		ns++;

 		pid=vvfork (NULL);

+fprintf (stderr, "\nDEBUG %s(%i):  ns = %i, pid = %i, a = %i, n_list = %i", __FILE__, __LINE__, ns, pid, a, n_list);

 		if ( pid==0)

 		{

 			int in;

 			initiate_vtmpnam (NULL);

 			CL->local_stderr=vfopen("/dev/null", "w");

 			in=CL->ne;

+fprintf (stderr, "\nDEBUG %s(%i):  in = %i, fname[a] = %s, in_mode = %s, mem_mode = %s, weight_mode = %s", __FILE__, __LINE__, in, fname[a], in_mode, mem_mode, weight_mode);

 			CL=read_constraint_list (CL, fname[a], in_mode, mem_mode,weight_mode);

 			if (CL->ne>in)dump_constraint_list(CL,tmp_list[a], "w");

+fprintf (stderr, "\nDEBUG %s(%i): before exit  in = %i", __FILE__, __LINE__, in);

 			myexit (EXIT_SUCCESS);

 		}

 		else

 		{

 			//set_pid (pid);

-			fprintf ( local_stderr, "\n\t--- Process Method/Library/Aln %s", fname[a], ns);

+			fprintf ( local_stderr, "\n\t--- Process Method/Library/Aln %s (ns=%i)", fname[a], ns);

 			proclist[pid]=a;

 			if (ns>=nproc)

 			{

 				b=proclist[vwait(NULL)];

 				fprintf (local_stderr, "\n\txxx Retrieved %s",fname[a]);

+fprintf (stderr, "\nDEBUG %s(%i): ns = %i, nproc = %i, tmp_list_b_%i_ = %s", __FILE__, __LINE__, ns, nproc, b, tmp_list[b]);

 				if (tmp_list[b] && check_file_exists (tmp_list[b]))

 				{

 					CL=undump_constraint_list(CL,tmp_list[b]);

@@ -2178,14 +2183,18 @@ Constraint_list* fork_read_n_constraint_

 	while (ns)

 	{

 		int pid2;

+fprintf (stderr, "\nDEBUG %s(%i): before vwait(): pid2 = %i", __FILE__, __LINE__, pid2);

 		pid2=vwait(NULL);

+fprintf (stderr, "\nDEBUG %s(%i): after vwait()", __FILE__, __LINE__);

 		a=proclist[pid2];

 		fprintf (local_stderr, "\n\txxx Retrieved %s",fname[a]);

+fprintf (stderr, "\nDEBUG %s(%i): n_list = %i, nproc = %i, tmp_list_a_%i_ = %s", __FILE__, __LINE__, ns, n_list, a, tmp_list[a]);

 		if (tmp_list[a] && check_file_exists (tmp_list[a]))

 		{

 			CL=undump_constraint_list (CL,tmp_list[a]);

 		}

 		ns--;

+fprintf (stderr, "\nDEBUG %s(%i):  ns = %i", __FILE__, __LINE__, ns);

 	}

 	fprintf ( local_stderr, "\n\n\tAll Methods Retrieved\n");

@@ -2216,11 +2225,20 @@ Constraint_list* read_constraint_list(Co

 	Sequence *SL=NULL, *TS=NULL;

 	int a;

 	Constraint_list *SUBCL=NULL;

-	static char *read_mode;

+	/*static char *read_mode;*/

+	static char read_mode[STRING];

 	char *fname;

+fprintf (stderr, "\nDEBUG %s(%i):  in_fname = %s, in_mode = %s, mem_mode = %s, weight_mode = %s", __FILE__, __LINE__, in_fname, in_mode, mem_mode, weight_mode);

 	fname=in_fname;

-	if ( !read_mode)read_mode=(char*)vcalloc ( STRING, sizeof (char));

+	/*if ( !read_mode)read_mode=(char*)vcalloc ( STRING, sizeof (char));*/

+

+if (read_mode)

+fprintf (stderr, "\nDEBUG %s(%i):  read_mode = %s, STRING = %i", __FILE__, __LINE__, read_mode, STRING);

+else

+fprintf (stderr, "\nDEBUG %s(%i):  STRING = %s, fname = %s", __FILE__, __LINE__, STRING, fname);

+sprintf ( read_mode, "structure");

+fprintf (stderr, "\nDEBUG %s(%i):  read_mode = %s, fname[0] = %c", __FILE__, __LINE__, STRING, fname[0]);

 	if ( is_lib_list (in_fname))sprintf ( read_mode, "lib_list");

 	else if ( in_mode)sprintf (read_mode, "%s", in_mode);

--- a/t_coffee_source/util_lib/util.c

+++ b/t_coffee_source/util_lib/util.c

@@ -4348,7 +4348,9 @@ pid_t vwait (pid_t *p)

   p2=wait(&rv); 

+fprintf (stderr, "\nDEBUG %s(%i): before check_process() p2 = %i", __FILE__, __LINE__, p2);

   if (p2!=-1)rv=check_process("forked::T-Coffee", p2, rv,handle_failure);

+fprintf (stderr, "\nDEBUG %s(%i): after check_process() p2 = %i", __FILE__, __LINE__, p2);

   if ( p) p[0]=rv;

   return p2;

@@ -4957,7 +4959,9 @@ int  set_unique_dir_4_tcoffee (char *dir

 void myexit (int signal)

 {

+fprintf (stderr, "\nDEBUG %s(%i): in myexit() signal = %i", __FILE__, __LINE__, signal);

   if (clean_exit_started==1)return; //protects processes while they are doing a clean exit

+fprintf (stderr, "\nDEBUG %s(%i): in myexit() signal = %i", __FILE__, __LINE__, signal);

   global_exit_signal=signal;

   exit (global_exit_signal); //ONLY BARE EXIT!!!!!!!!!!!!!!

 }

@@ -5589,6 +5593,7 @@ void dump_tcoffee(char *target, char *na

   char *out_list;

+fprintf (stderr, "\nDEBUG %s(%i): dump_tcoffee() target = %s, nature = %s, pid = %i, ppid = %i", __FILE__, __LINE__, target, nature, getpid(), getppid());

   if ((fp=fopen (target, "w")))

     {

@@ -5663,6 +5668,8 @@ void dump_error_file()

   FILE *fp;

+fprintf (stderr, "\nDEBUG %s(%i): dump_error_file() pid = %i, ppid = %i", __FILE__, __LINE__, getpid(), getppid());

+

   sprintf ( target, "%s",getenv("ERRORFILE_4_TCOFFEE"));

   if (strstr (target, "NO"));

   else

@@ -8962,6 +8969,9 @@ void clean_exit ()

   Tmpname *start;

   int debug;

+fprintf (stderr, "\nDEBUG %s(%i): clean_exit() pid = %i, ppid = %i", __FILE__, __LINE__, getpid(), getppid());

+/* https://stackoverflow.com/questions/26256996/who-called-atexit */

+/* abort(); */

   clean_exit_started=1;//prevent new locks

   start=tmpname;

   //1-start killing all the children

@@ -8979,6 +8989,7 @@ void clean_exit ()

   if (is_rootpid())

     {

+fprintf (stderr, "\nDEBUG %s(%i): clean_exit() / is_rootpid()=true: pid = %i, ppid = %i", __FILE__, __LINE__, getpid(), getppid());

       kill_child_pid(getpid());

       if (has_error_lock())

@@ -8988,6 +8999,7 @@ void clean_exit ()

 	  warning_msg (stderr);

 	  e=lock (getpid(), LERROR, LREAD, NULL);

+fprintf (stderr, "\nDEBUG %s(%i): clean_exit() / has_error_lock()=true: e = '%s'\n", __FILE__, __LINE__, e);

 	  //explicit the most common error messages

--- a/t_coffee_source/t_coffee_lib/t_coffee.c

+++ b/t_coffee_source/t_coffee_lib/t_coffee.c

@@ -4762,7 +4762,9 @@ get_cl_param(\

 		     }

 		   else

 		     {

+fprintf (stderr, "\nDEBUG %s(%i): before read_n_constraint_list(): infile = %s", __FILE__, __LINE__, infile);

 		     CL=read_n_constraint_list (list_file,n_list,NULL, mem_mode,weight,type, le, CL, seq_source);

+fprintf (stderr, "\nDEBUG %s(%i): after read_n_constraint_list(): infile = %s", __FILE__, __LINE__, infile);

 		     }

 		 }

 	       if ( CL->M)clean_aln=0;

stable-linking-inputs.patch

clustalw2.patch

gcc-7.patch

# debug.patch